Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate WP_049757088.1 ADEG_RS01960 hypothetical protein
Query= curated2:P05378 (462 letters) >NCBI__GCF_000024605.1:WP_049757088.1 Length = 268 Score = 124 bits (310), Expect = 5e-33 Identities = 88/228 (38%), Positives = 109/228 (47%), Gaps = 20/228 (8%) Query: 69 ERVETRDPLRALYERVYAPLERHPDLP-----PFFGGVVGYAAYDLVRYYERLPSLKPDD 123 E E DPL L + L RH P PF GG G+ +YDL R ER+PS DD Sbjct: 44 EWTEEGDPLELLRD-----LLRHYQYPSGCPLPFCGGAAGFISYDLGRQLERIPSRALDD 98 Query: 124 LGLPDLLFVEPEVVAVFDHLKNLLHLVAPG---RDPEEAEARLFWAERRLKG------PL 174 L PD + V D L + LVA G ++P +A+ R L PL Sbjct: 99 LSTPDFYLGFYDTALVVDELSREVFLVATGLPEKEPCQAQKRALARAAELSELIRNITPL 158 Query: 175 PGVPGERAGGRARFQADFSREAYLEAVRRALDYIRAGDIFQVVLSLRLSSPLTVHPFALY 234 P P A F +Y EAV RA +YI AGDIFQV LS R S P + +Y Sbjct: 159 PP-PRPLPAQECPLYAHFDASSYCEAVTRAKEYIAAGDIFQVNLSQRFSLPRLFDSWEVY 217 Query: 235 RALRSVNPSPYMGYLDLGEVVLVSASPESLLRSDGRRVVTRPIAGTRP 282 LR +NP+P YL+LGE +V ASPE L+ RV TRP+ + P Sbjct: 218 LRLREINPAPMAAYLNLGEWQIVPASPERFLQVRNGRVETRPVTSSPP 265 Score = 24.3 bits (51), Expect = 0.005 Identities = 12/29 (41%), Positives = 19/29 (65%), Gaps = 2/29 (6%) Query: 431 IVADSVPEREYEECWNKARALLKAVEMAE 459 +VA +PE+E C + RAL +A E++E Sbjct: 124 LVATGLPEKE--PCQAQKRALARAAELSE 150 Lambda K H 0.321 0.139 0.408 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 300 Number of extensions: 13 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 462 Length of database: 268 Length adjustment: 29 Effective length of query: 433 Effective length of database: 239 Effective search space: 103487 Effective search space used: 103487 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory